I used Calibre to convert an lrf to epub. In doing so, the book ended up with a duplicate cover. So, I installed Sigil and deleted the second cover picture and page break, and saved it. I was surprised to see that in the resulting epub file, the text is smaller. Just to test, I opened the Calibre-created epub in Sigil and re-saved it without making any changes, and sure enough, the font size got smaller. Why is this happening? Also, what other changes are being made to the document when it passes through Sigil?

I have also noticed that if I am editing an imported ePub file and I delete a space between sentences it often changes the font of the sentence after the deleted space????

You probably had a span tag (with styles applied) wrapped around that sentence, and now you've merged the other sentence into that span tag. Naturally, the other sentence now has those same styles too.